Fast algorithms for toeplitz and hankel matrices georg heinig and karla rost abstract the paper gives a selfcontained survey of fast algorithms for solving linear systems of equations with toeplitz or hankel coe cient matrices. Hypergraph partitioning for parallel sparse matrixmatrix multiplication. We have also performed a comparison with other reordering algorithms. If p is a sparse matrix, then both representations use storage proportional to n and you can apply either to s in time proportional to nnzs. I wonder if there are other forms used in computational problems encountered in physics, chemistry, etc. Sparse matrix reordering consists of swapping the matrix rows and columns in order to reduce the fillin orand the matrix bandwidth. Sparse matrix and its representations set 1 using arrays and linked lists a matrix is a twodimensional data object made of m rows and n columns, therefore having total m x n values.
Parallelization of reordering algorithms for bandwidth and. The main benefits of reordering are calculation speedup and memory storage reduction. Permutation and reordering sparse matrices mathematics. From this, a simple algorithm can be constructed which loops over the indices i from 1 through n and j from. A permutation of the rows and columns of a sparse matrix s can be represented in two ways. Then ab is a simple sparse matrix size 3x3 in the example. The a subblocks are rolled one step to the left and the b. These aim to keep the number of extra entries that are filled in during lufactorization small. Algorithms for structured matrixvector product of optimal. So if you pick an ordering, like approximate minimum degree and you pick a matrix like this one and you run ive been very interested in that. The definition of matrix multiplication is that if c ab for an n.
Matrix reordering is not only useful for speedup but often mandatory in order to obtain a code which runs in a reasonable amount of time, especially for sparse direct solvers. In this paper we examine the cuthillmckee algorithm for ordering the. First, the matrix a is ordered by some fillreducing ordering. A fast algorithm for reordering sparse matrices for. The implementation is based closely on the sparspak implementation described by george and liu.
Reordering the reorderable matrix as an algorithmic problem erkkim. Many applications in computational science rely on algorithms for largescale sparse. The gibbspoolestockmeyer and gibbsking algorithms for reordering sparse matrices. Reordering was originally developed for direct methods but it has recen. Comparative analysis of the cuthillmckee and the reverse cuthill. Step 1take the middle n2,m2 of the matrix and compare it to the value step 2 if the value equals mi,j return i,j step 3 if the value is higher you can get rid from the first quarter step 4 if the value is lower you can get rid from the forth quarter step 5 split the 3 other quarters to 2, a rectangle and a box, send those both. Routines to read and write sparse matrices using a simple file format with one line per nonzero, specifying the row, column, and value.
Except for the c 2 105 case, the rmat matrix has more nonzeros than the righthand matrix. Then use the identifiers to create the ordered block matrix aperm from abperm and youll have the desired result, i believe. On page 3 of this document, there are some matrix forms for sparse matrices. The full restriction operation of order 8 applied to a scale 23 rmat matrix. A permutation vector p, which is a full vector containing a permutation of 1. In proceedings of the 27th acm on symposium on parallelism. Course home syllabus calendar readings assignments projects study materials video.
We propose several parallel algorithms for such applications based on ideas from cyclic reduction, dynamic programming, and nested dissection. We then do elimination, which factors in l times u probably l. Reordering the reorderable matrix as an algorithmic problem. You take the matrix, k to d, you take the permutation that comes from approximate minimum degree, that gives you this reordered matrix. In many applications measured data can be represented in a matrix x m. The remainder of this paper is organized as follows. A preliminary version of parts of this paper, in particular the main algorithm and main theorem of section 3, appeared as. The number of zerovalued elements divided by the total number of elements e. Algorithm 5 toeplitzplushankel matrixvector product 1.
Github slafisparsematrixreorderingusingrcmalgorithm. Sparse matrix computations paperback september 23, 2014 by james r. The algorithm treats the matrix as the adjacency matrix of a graph, coarsens the graph by collapsing vertices and edges, reorders the smaller graph, and then uses refinement steps to uncoarsen the small graph and produce a reordering of the original graph. This makes the algorithms prohibitive for large scale computations. The basic algorithms, such as matrix multiplication are simple enough to invite total comprehension, yet. The vector representation is slightly more compact and efficient, so the various sparse matrix permutation routines all return full row vectors with the exception of the pivoting permutation in lu triangular factorization, which returns a matrix.
The algorithm first finds a pseudoperipheral vertex of the graph of the matrix. Special topics in sparse matrix algorithms department of computer science and engineering spring 2015 syllabus tim davis last modi ed september 23, 2014 1 catalog description csce 689. Given two sparse matrices sparse matrix and its representations set 1 using arrays and linked lists, perform operations such as add, multiply or transpose of the matrices in their sparse form itself. Bring machine intelligence to your app with our algorithmic functions as a service api. Reordering matrices for optimal sparse matrix bipartitioning. Sparse matrix algorithms solve lx b with l unit lower triangular. Implementing sparse matrices for graph algorithms author. Preconditioning sparse matrices for computing eigenvalues. Many algorithms can be used to reorder sparse matrices. From this, a simple algorithm can be constructed which loops over the indices i from 1 through n and j from 1 through p, computing the above using a nested loop.
In numerical linear algebra, the cuthillmckee algorithm cm, named for elizabeth cuthill and james mckee, is an algorithm to permute a sparse matrix that has a symmetric sparsity pattern into a band matrix form with a small bandwidth. Your matrices are probably too small for sparse algorithms to be worthwhile, so the only other opportunities for faster algorithms would require additional matrix structure e. Matrix block structure in sparse matrixvector multiplication. The book contains an introduction to matrix analysis, and to the basic algorithms of numerical linear algebra. Parmetis a library for graphpartitioning, but provides matrix reordering algorithms as well. Here youll find current best sellers in books, new releases in books, deals in books, kindle ebooks, audible audiobooks, and so much more. The new reordering algorithm using rotation is shown to produce trees with. Spectral regularization algorithms for learning large. In numerical analysis and scientific computing, a sparse matrix or sparse array is a matrix in which most of the elements are zero. A survey of direct methods for sparse linear systems tamu. The thorough explanations has necessarily restricted the scope of the series, but topic selection gives the reader a sound basis for further study. We propose alternative data structures, as well as reordering algorithms to increase the effectiveness of those data structures, to reduce the number of memory indirections in spmxv. Parallel algorithms for sparse matrix product, indexing, and.
Many sparse matrix computations can be speeded up if the matrix is first reordered. In proceedings of the 27th acm on symposium on parallelism in algorithms and architectures, spaa 15, pages 8688. We consider the problem of finding equivalent reorderings of a sparse matrix so. Preconditioning sparse matrices for computing eigenvalues and. The problem is to complete the matrix based on the observed entries, and has been dubbed the matrix completion problem ccs08, cr08, rfp07, ct09, kom09, rs05.
All algorithms in this paper have been shown to be the fastest possible in terms of bilinear complexity. Performance analysis rows of alltoall broadcasts, each is among a group of processes. A 6 6 sparse matrix a on the left and its corresponding hypergraph for the sparsematrix partitioning problem. The proofs may be found in 14 and involve determining the tensor ranks of.
The book of horn and johnson hj85 is an excellent reference for theoretical results about matrix analysis. If most of the elements of the matrix have 0 value, then it is called a sparse matrix. Improving the locality of the sparse matrixvector product on shared. This is in contrast to a dense matrix, where many or most of the elements have a nonzero value. Second, a parallel ordering of a is computed from the filled graph that results from symbolically factoring a using the. Reordering sparse matrices for parallel elimination sciencedirect. We consider three general classes of algorithms for generating orderings. All content, all journals, all books, all proceedings, this journal. This library provides first sparse matrix computation kernels including spmv and spgemm. University of california, berkeley 1998 a dissertation submitted in partial satisfaction of the requirements for the degree of. The paper examines techniques for solving linear systems represented by dense matrices. This paper has been followed by a lot of algorithms, one. A comparison of vertex ordering algorithms for large graph.
This page contains the documents abstract and table of contents. The result should consist of three sparse matrices, one obtained by adding the two input matrices, one by multiplying the two matrices and. Algorithm 5 toeplitzplushankel matrix vector product 1. Algorithms of levinsontype and of schurtype are discussed. Preprocessing overhead for matrix reordering should be amortizable via the gain in computation step. The reordering algorithms were tested for a broad set of matrices. Each block is sent to each process, and the copied sub blocks are multiplied together and the results added to the partial results in the c subblocks. Computing inverse elements for a large matrix requires a lot of memory and is very timeconsuming even using our e cient algorithm with optimization. It then generates a level structure by breadthfirst search and orders the vertices by decreasing distance from the pseudoperipheral vertex.
Matrixvector multiplication, triangular solvers, matrix reordering. Create a matrix of processes of size p12 12 x p so that each process can maintain a block of a matrix and a block of b matrix. Preconditioning sparse matrices for computing eigenvalues and solving linear systems of equations by tzuyi chen b. Matrix methods have important applications in many scienti. This book is composed of six parts encompassing 27 chapters that contain contributions in several areas of matrix computations and some of the most potential research in numerical linear algebra. Algorithms for reordering sparse matrices play a vital role in our ability to. The books homepage helps you explore earths biggest bookstore without ever leaving the comfort of your couch. By contrast, if most of the elements are nonzero, then the matrix is considered dense. Graph working on the adjacency graph directly and provides some ordering algorithms, like the mentioned cuthillmckee, and minimumdegree ordering ptscotch for graphpartitioning and sparse matrix reordering.
Computing a compressed approximate matrix decomposition, by p. This paper investigates the performance of sparse matrix multiplication kernels on two leading highperformance computing architectures intels knights landing processor and nvidias pascal gpu. Improving performance of sparse matrixvector multiplication. Sparse matrix and its representations set 1 using arrays. A sparse matrix is a matrix in which many or most of the elements have a value of zero. Toledo 7 proposed identifying 1 2 blocks of a matrix and writing the matrix as the sum of two matrices, the. Sparse matrix computations is a collection of papers presented at the 1975 symposium by the same title, held at argonne national laboratory. A spectral algorithm for envelope reduction of sparse matrices. The dissect function uses graphtheoretic techniques to produce fillreducing orderings. A permutation matrix p acts on the rows of s as ps or on the columns as sp. Section 2 discusses the shortcomings of current sparse matrix data structures and proposes new alternatives.
You can then use the reverse cuthillmckee ordering to get the permutations you want, and apply these permutations to ab. Feb 19, 2014 a seminar given at stanford in june 20. The proofs may be found in 14 and involve determining the tensor ranks of these structured matrixvector products. We describe a data placement method and a chunkingbased algorithm for our kernels that exploits the existence of the multiple memory spaces in each. Sparse matrix computation is a key kernel of many applications. Sparse matrix algorithms stanford, june 20, tim davis.